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FAIR in practice reference list
<p>This is a collection of information curated by the FAIR Practice Task Force of the EOSC FAIR Working Group.</p> <p>It aims to provide a reading list of published information on efforts to apply the FAIR principles.</p> <p>Please read the README tab in the spreadsheet for instructions on how to use this resource.</p>
BAGS: an automated barcode, audit & grade system for DNA barcode reference libraries
<p>Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here we present an R-based application, BAGS (Barcode, Audit & Grade System; https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in Barcode Index Numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.</p>
Fig 5 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 5. Neighbour-joining tree showing all available DNA barcodes for species in family Rhinolophidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, JV = Java Indonesia, IND = India, CH = China, CM = Cambodia, MN = Myanmar. https://doi.org/10.1371/journal.pone.0179555.g005
Fig 4 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 4. Neighbour-joining tree showing all available DNA barcodes for species in family Hipposideridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China, CM = Cambodia. https://doi.org/10.1371/journal.pone.0179555.g004
Fig 2 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 2. Neighbour-joining tree showing all available DNA barcodes for species in family Pteropodidae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, JV = Java, Indonesia, BN = Borneo (including Sabah, Sarawak, Brunei and Kalimantan), TH = Thailand, LA = Laos. https://doi.org/10.1371/journal.pone.0179555.g002
Fig 3 in A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
Fig 3. Neighbour-joining tree showing all available DNA barcodes for species in families Emballonuridae, Megadermatidae, Molossidae and Nycteridae reported from Peninsular Malaysia. The percentage of pseudoreplicate trees (±70%) in which the DNA barcodes clustered together in the bootstrap test (500 pseudoreplicates) are shown above the branches. Abbreviation as follows: PM = Peninsular Malaysia, VN = Vietnam, BN = Borneo (including Sabah & Sarawak of East Malaysia, Brunei and Kalimantan Indonesia), TH = Thailand, LA = Laos, SM = Sumatera Indonesia, CH = China. https://doi.org/10.1371/journal.pone.0179555.g003
Reference data for MITOS2
<p>Reference data for MITOS2 derived from RefSeq63 and 81 separately for Metazoa (m), Fungi (f), and Opisthokonta (o).</p> <p>Contains</p> <p>- fasta databases for the BLAST searches</p> <p>- automatically derived covariance models for RNA searches</p> <p>- for refseq63m hidden markov models for protein prediction (http://dx.doi.org/10.1016/j.ympev.2016.09.024)</p> <p> </p>
dataset for paper Vanhaebost J, Faouzi M, Mangin P, Michaud K: New reference tables and user-friendly Internet application for predicted heart weights. Int J Legal Med 2014, 128(4):615-620.
<p>The heart weight is the most important parameter in the determination of cardiac hypertrophy. The obtained heart weight value should be compared against tables of normal weights by age, gender and body weight and height</p> <p>In the study by Vanhaebost<em> et al</em>. has been shown in the Swiss population that the heart weight increases along with the increase of the body weight, body height, BMI and body surface area (BSA). The mean heart weight is greater in men than in women at a similar body weight. The reference tables for predicted heart weights obtained from this study are presented as an user-friendly internet application (<a href="http://calc.chuv.ch/Heartweight">http://calc.chuv.ch/Heartweight</a>) enabling the comparison of heart weights observed at autopsy with the reference values.</p>
The Neogene 2020 reference dataset (De Nil et al., 2020)
<p>Table 2, Table 3 and Table 4 as the resulting dataset from 'De Nil, K., De Ceukelaire, M. & Van Damme, M., 2020. A reference dataset for the Neogene lithostratigraphy in Flanders, Belgium. Geologica Belgica, 23/3-4. <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.20341%2Fgb.2020.021&data=04%7C01%7Ckatrien.denil%40vlaanderen.be%7Cb6f4944eb0d54af5762308d896026f24%7C0c0338a695614ee8b8d64e89cbd520a0%7C0%7C0%7C637424284489463336%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=vZAilldByLDJ7KhLFQ2z8ajnapX53lea4Zfh2YAAFGo%3D&reserved=0">https://doi.org/10.20341/gb.2020.021</a>'</p> <p><strong>Table</strong><strong> 2.</strong> The general and different (sub)reference datasets resulting from the individual Neogene 2020 papers, with their DOV URL.</p> <p><strong>Table 3.</strong> List of the individual boreholes and (temporary) outcrops of the Neogene reference set, with reference to the different individual papers of this collection, sorted by location as mentioned in the papers. *Complete ‘<a href="https://www.dov.vlaanderen.be/data/">https://www.dov.vlaanderen.be/data/</a>boring/’ with this unique code. **Complete <a href="http://collections.naturalsciences.be/ssh-geology-archives/arch/">http://collections.naturalsciences.be/ssh-geology-archives/arch/</a> with this unique code.</p> <p><strong>Table 4</strong>. List of the individual CPT’s with reference to the different individual papers of this collection, sorted by DOV name.</p>
BAM reference data: SEM raw data for the Particles Size Distribution of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a)
<p>The SEM images are given in the TIF format.</p> <p>For further information please look at:</p> <p>- Radnik, J. Kersting, R., Hagenhoff, B., Bennet, F., Ciornii, D.; Nymark, P., Grafström R. and Hodoroaba, V.- D. <em>Nanomaterials </em><strong>2021</strong>, <em>11</em>, 639. https://doi.org/10.3390/nano11030639, and</p> <p>- Vasile-Dan Hodoroaba. (2021). BAM reference data: EDS raw data of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4986420</p> <p>- Radnik, Jörg. (2021). BAM reference data: XPS raw data of Al-coated titania nanoparticles (JRCNM62001a and JRCNM62002a) [Data set]. Nanomaterials. Zenodo. http://doi.org/10.5281/zenodo.4986068</p> <p>Measurement conditions:</p> <p>In the present work, a SEM of type Supra 40 (ZEISS, Oberkochen, Germany) with a Schottky field emitter and an InLens secondary electron detector was used at a 5 kV beam acceleration voltage.</p>
picardmetrics: Reference files
<p>Reference files used to test picardmetrics:</p> <ol> <li>gencode.v19.annotation.refFlat</li> <li>gencode.v19.annotation.rRNA.interval_list</li> <li>iGenomes.UCSC.hg19.genome.fa</li> </ol> <p>picardmetrics: https://github.com/slowkow/picardmetrics</p>
Liftover of DGRP D.melanogaster genotypes to reference genome assembly v6.0, with QC graph
<p>Output are vcf and plink-format genotype files. Also provided are the run code in bash and R, the logs, summary statistics, and a graph showing how the positions of SNPs have changed.</p>
Audio files of beat note between WWV-10 carrier wave and GPS reference signal
<p>NAME : Martin Potter, VE3OAT<br> GEOPOSIT : 45 15' 9.023" N 75 35' 27.60" W (Maidenhead FN25eg)<br> START TIME : 1400 UT<br> STATION CONFIG :<br> Multi-band vertical antenna with 18 radials.<br> Receiver Yaesu FTdx1200 in AM mode with audio bandwidth limited to<br> 800-1200 Hz (18 dB/octave roll-off).<br> Trimble Thunderbolt 10 MHz output to HP 3325B sig generator set<br> to 9999 kHz and injected to station antenna.<br> Measured nominal 1 kHz beat note between WWV-10 and sig generator<br> using SpectrumLab software. Audio WAV file recorded by SpectrumLab. <br> <br> Note : On 20 Aug, receiver AGC was ON. On 21 Aug, receiver AGC was<br> OFF and audio output level was set using RF Gain control. </p> <p> </p>
Supplementary tables for publication "A reference-free algorithm discovers regulation in the plant transcriptome"
<p>Supplementary tables for publication "A reference-free algorithm discovers regulation in the plant transcriptome" (doi: https://doi.org/10.1101/2024.05.23.595613)</p> <p>Table A: complete list of significant anchors and associated genes from analysis of sorghum dataset</p> <p>Table B: complete list of significant anchors and associated genes from analysis of maize dataset</p> <p>Table C: complete list of significant anchors and associated genes from analysis of Arabidopsis P/Fe dataset</p> <p>Table D: complete list of significant anchors and associated genes from analysis of Arabidopsis FLOE1 dataset</p> <p>arabidopsis_floe1_ALL_anchors_satc_truncated.txt: data from the Arabidopsis FLOE1 dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>arabidopsis_pfe_ALL_anchors_satc_truncated.txt: data from the Arabidopsis P/Fe dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>maize_pollen_ALL_anchors_satc_truncated.txt: data from the maize dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample. </p> <p>sorghum_drought_ALL_anchors_satc_truncated.txt: data from the sorghum dataset used to generate figures in the paper. Columns are sample ID, anchor, target, and counts of that anchor/target combination in that particular sample.</p> <p>cryptic_splicing_anchors.tsv: list of anchors described in Supplementary Information section of the article that are examples of cryptic splicing. Columns are dataset name, gene name/ID, anchor sequence, target 1 sequence, and target 2 sequence. </p>
Dataset for comparison of QuantumPower method to the reference power standard
<p>Dataset for comparison of QuantumPower method to the power standard Radian RD-22.</p> <p>The QuantumPower method was compared to a power standard Radian RD-22. As a device under test, a Fluke 6100 power calibrator was used.</p> <p>To obtain the data, QPSW software was used:</p> <p>https://github.com/KaeroDot/QPsw</p> <p>Author: Martin Šíra</p> <p>Contact: Czech Metrology Institute, Okružní 31, 638 00 Brno, msira@cmi.cz</p> <p>Part of project Quantum traceability for AC power standards, QuantumPower, Project Number: 19RPT01.<em> </em>This project (19RPT01) has received funding from the EMPIR programme co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation programme.</p> <p>https://www.euramet.org/research-innovation/search-research-projects/details/project/quantum-traceability-for-ac-power-standards/</p>
Fig. 7 in Revision of the Small Tropical Whipsnakes Previously Referred to Demansia olivacea (Gray, 1842) and Demansia torquata (Günther, 1862) (Squamata: Elapidae)
Fig. 7. Demansia flagellatio from Riversleigh World Heritage fossil site, Boodjamulla (Lawn Hill) National Park; freshly-dead specimen.
Fig. 5 in Revision of the Small Tropical Whipsnakes Previously Referred to Demansia olivacea (Gray, 1842) and Demansia torquata (Günther, 1862) (Squamata: Elapidae)
Fig. 5. Head shields and colour pattern of the head and neck of the holotype of Demansia calodera, in dorsal, left lateral and ventral views. Scale bar = 3 mm.
Fig. 3 in Revision of the Small Tropical Whipsnakes Previously Referred to Demansia olivacea (Gray, 1842) and Demansia torquata (Günther, 1862) (Squamata: Elapidae)
Fig. 3. Distribution of Demansia angusticeps (solid dots), D. calodera (solid squares) and D. flagellatio (solid triangles).
Fig. 12 in Revision of the Small Tropical Whipsnakes Previously Referred to Demansia olivacea (Gray, 1842) and Demansia torquata (Günther, 1862) (Squamata: Elapidae)
Fig. 12. Head shields and colour pattern of the head and neck of the holotype of Demansia quaesitor in dorsal, right lateral and ventral views. Scale bar = 3 mm.
Fig. 20 in Revision of the Small Tropical Whipsnakes Previously Referred to Demansia olivacea (Gray, 1842) and Demansia torquata (Günther, 1862) (Squamata: Elapidae)
Fig. 20. Head shields and colour pattern of the head and neck of Demansia torquata (AM R114086) in dorsal, left lateral and ventral views. Scale bar = 3 mm.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.